# Bio.PopGen.GenePop.EasyController module

Control GenePop through an easier interface.

This interface is less efficient than the standard GenePopControler

class Bio.PopGen.GenePop.EasyController.EasyController(fname, genepop_dir=None)

  Bases: `object`

  Define a class for an easier interface with the GenePop program.

  __init__(fname, genepop_dir=None)

    Initialize the controller.

    genepop_dir is the directory where GenePop is.

    The binary should be called Genepop (capital G)

  get_basic_info()

    Obtain the population list and loci list from the file.

  test_hw_pop(pop_pos, test_type='probability')

    Perform Hardy-Weinberg test on the given position.

  test_hw_global(test_type='deficiency', enum_test=True, dememorization=10000, batches=20, iterations=5000)

    Perform Hardy-Weinberg global Heterozygote test.

  test_ld_all_pair(locus1, locus2, dememorization=10000, batches=20, iterations=5000)

    Test for linkage disequilibrium for each pair of loci in each population.

  estimate_nm()

    Estimate Nm. Just a simple bridge.

  get_heterozygosity_info(pop_pos, locus_name)

    Return the heterozygosity info for a certain locus on a population.

    Returns (Expected homozygotes, observed homozygotes, Expected heterozygotes, observed heterozygotes)

  get_genotype_count(pop_pos, locus_name)

    Return the genotype counts for a certain population and locus.

  get_fis(pop_pos, locus_name)

    Return the Fis for a certain population and locus.

    Below CW means Cockerham and Weir and RH means Robertson and Hill.

    Returns a pair:

    - dictionary [allele] = (repetition count, frequency, Fis CW ) with information for each allele

    - a triple with total number of alleles, Fis CW, Fis RH

  get_alleles(pop_pos, locus_name)

    Return the alleles for a certain population and locus.

  get_alleles_all_pops(locus_name)

    Return the alleles for a certain population and locus.

  get_allele_frequency(pop_pos, locus_name)

    Calculate the allele frequency for a certain locus on a population.

  get_multilocus_f_stats()

    Return the multilocus F stats.

    Explain averaging. Returns Fis(CW), Fst, Fit

  get_f_stats(locus_name)

    Return F stats for a locus.

    Returns Fis(CW), Fst, Fit, Qintra, Qinter

  get_avg_fis()

    Calculate identity-base average Fis.

  get_avg_fst_pair()

    Calculate Allele size-base average Fis for all population pairs.

  get_avg_fst_pair_locus(locus)

    Calculate Allele size-base average Fis for all population pairs of the given locus.

  calc_ibd(is_diplo=True, stat='a', scale='Log', min_dist=0.00001)

    Calculate isolation by distance statistics for Diploid or Haploid.

  __firstlineno__ = 19
  __static_attributes__ = ('__allele_frequency', '__fst_pair_locus', '_controller', '_fname')

Biopython v: 1.85

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